The analog pins are not routed through FPGA. They are connected to both - FPGA and SAMD.

The Cyclone 10 LP lacks any analog capabilities, so it's physically impossible for it to route analog stuff.

Using the analog inputs on SAMD side should be totally ok, as long as you're not configuring same pins as outputs on the FPGA side.

Depending on the FPGA configuration image used, unused pins on FPGA side could be configured as input tri-stated with weak pullups (25 kΩ typical value) . The high-impedance sources might end up being measured incorrectly because of that.